mlsanityData to 7 Oct 2026

BERN2: an advanced neural biomedical named entity recognition and normalization tool

arXiv 2201.02080 ↗First posted 6 Jan 2022cs.CLcited by 42

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Abstract (arXiv)

In biomedical natural language processing, named entity recognition (NER) and named entity normalization (NEN) are key tasks that enable the automatic extraction of biomedical entities (e.g. diseases and drugs) from the ever-growing biomedical literature. In this article, we present BERN2 (Advanced Biomedical Entity Recognition and Normalization), a tool that improves the previous neural network-based NER tool by employing a multi-task NER model and neural network-based NEN models to achieve much faster and more accurate inference. We hope that our tool can help annotate large-scale biomedical texts for various tasks such as biomedical knowledge graph construction.

Key facts. Cited by 42 papers in the map (data through 7 Oct 2026). Builds on 8 of its 37 references that are in the map. First posted on arXiv 6 Jan 2022.

Builds on

8 of 37 references.

References · 8

  1. 2017Billion-scale similarity search with GPUscited by 2,477
  2. 2019BioBERT: a pre-trained biomedical language representation model for biomedical text miningcited by 1,935
  3. 2020Domain-Specific Language Model Pretraining for Biomedical Natural Language Processingcited by 996
  4. 2020Biomedical Entity Representations with Synonym Marginalizationcited by 59
  5. 2020Building a PubMed knowledge graphcited by 38
  6. 2018Cross-type Biomedical Named Entity Recognition with Deep Multi-Task Learningcited by 28
  7. 2020HunFlair: An Easy-to-Use Tool for State-of-the-Art Biomedical Named Entity Recognitioncited by 26
  8. 2020Vapur: A Search Engine to Find Related Protein-Compound Pairs in COVID-19 Literaturecited by 3

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Cited by year (2026 to 7 Oct)

Citing papers per year: 2022: 3; 2023: 12; 2024: 15; 2025: 4; 2026: 8.

42 papers.

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  1. 2023BioT5: Enriching Cross-modal Integration in Biology with Chemical Knowledge and Natural Language Associationscited by 100
  2. 2022SciFact-Open: Towards open-domain scientific claim verificationcited by 94
  3. 2023MolXPT: Wrapping Molecules with Text for Generative Pre-trainingcited by 81
  4. 2024BioT5+: Towards Generalized Biological Understanding with IUPAC Integration and Multi-task Tuningcited by 54
  5. 2024Graph-Based Retriever Captures the Long Tail of Biomedical Knowledgecited by 20
  6. 2023LIQUID: A Framework for List Question Answering Dataset Generationcited by 19
  7. 2024A Fine-tuning Dataset and Benchmark for Large Language Models for Protein Understandingcited by 19
  8. 2023Enhancing Phenotype Recognition in Clinical Notes Using Large Language Models: PhenoBCBERT and PhenoGPTcited by 17
  9. 2024Leveraging Biomolecule and Natural Language through Multi-Modal Learning: A Surveycited by 16
  10. 2024PRESTO: Progressive Pretraining Enhances Synthetic Chemistry Outcomescited by 14
  11. 2024Few-shot clinical entity recognition in English, French and Spanish: masked language models outperform generative model promptingcited by 12
  12. 2023Exploring the In-context Learning Ability of Large Language Model for Biomedical Concept Linkingcited by 11
30 more
  1. 20243D-MolT5: Leveraging Discrete Structural Information for Molecule-Text Modelingcited by 9
  2. 2024HunFlair2 in a cross-corpus evaluation of biomedical named entity recognition and normalization toolscited by 8
  3. 2023BELB: a Biomedical Entity Linking Benchmarkcited by 7
  4. 2024Large Language Models Struggle in Token-Level Clinical Named Entity Recognitioncited by 7
  5. 2024BELHD: Improving Biomedical Entity Linking with Homonoym Disambiguationcited by 4
  6. 2022Biomedical NER for the Enterprise with Distillated BERN2 and the Kazu Frameworkcited by 3
  7. 2024A Simplified Retriever to Improve Accuracy of Phenotype Normalizations by Large Language Modelscited by 3
  8. 2024Y-Mol: A Multiscale Biomedical Knowledge-Guided Large Language Model for Drug Developmentcited by 3
  9. 2024Augmenting Biomedical Named Entity Recognition with General-domain Resourcescited by 2
  10. 2025BALI: Enhancing Biomedical Language Representations through Knowledge Graph and Language Model Alignmentcited by 2
  11. 2022Enhancing Label Consistency on Document-level Named Entity Recognitioncited by 1
  12. 2023Simple Data Augmentation Techniques for Chinese Disease Normalizationcited by 1
  13. 2023Learning a Patent-Informed Biomedical Knowledge Graph Reveals Technological Potential of Drug Repositioning Candidatescited by 1
  14. 2023Enhancing Low-resource Fine-grained Named Entity Recognition by Leveraging Coarse-grained Datasetscited by 1
  15. 2023Diversifying Knowledge Enhancement of Biomedical Language Models using Adapter Modules and Knowledge Graphscited by 1
  16. 2024Taec: a Manually annotated text dataset for trait and phenotype extraction and entity linking in wheat breeding literaturecited by 1
  17. 2025Privacy Meets Explainability: Managing Confidential Data and Transparency Policies in LLM-Empowered Sciencecited by 1
  18. 2025TrialMatchAI: An End-to-End AI-powered Clinical Trial Recommendation System to Streamline Patient-to-Trial Matchingcited by 1
  19. 2023EasyNER: A Customizable Easy-to-Use Pipeline for Deep Learning- and Dictionary-based Named Entity Recognition from Medical and Life Science Textcited by 0
  20. 2023Investigating Deep-Learning NLP for Automating the Extraction of Oncology Efficacy Endpoints from Scientific Literaturecited by 0
  21. 2024Hybrid X-Linker: Automated Data Generation and Extreme Multi-label Ranking for Biomedical Entity Linkingcited by 0
  22. 2025DREaM: Drug-Drug Relation Extraction via Transfer Learning Methodcited by 0
  23. 2026FigEx2: Visual-Conditioned Panel Detection and Captioning for Scientific Compound Figurescited by 0
  24. 2026Improving Large Molecular Language Model via Relation-aware Multimodal Collaborationcited by 0
  25. 2026BioBridge: Bridging Proteins and Language for Enhanced Biological Reasoning with LLMscited by 0
  26. 2026Self-Driving Datasets: From 20 Million Papers to Nuanced Biomedical Knowledge at Scalecited by 0
  27. 2026Knowledge-to-Verification: Exploring RLVR for LLMs in Knowledge-Intensive Domainscited by 0
  28. 2026Beyond Agreement: Scoring Panel-Surfaced Biomedical Entity Candidates for Curator Triagecited by 0
  29. 2026Automatic bioinformatic software named entity recognition from literaturecited by 0
  30. 2026BELXTR: Biomedical Entity Linking via Contextualized Token Retrievalcited by 0